The Bitter Flesh
by crookshanks11
Summary: The Doctor starts acting odd - very odd - and Amy and Rory are left muddled. When he becomes hostile, will they finally leave him or find the meaning behind his strange behavior? Spoilers for Series 6. Rated T for mild violence and sexual references.
1. Chapter 1

**Takes place after "The Doctor's Wife" but before "The Rebel Flesh"**

"How about Paris? I've never actually been there before," Amy suggested.

The Doctor circled the TARDIS console, typing coordinates and pulling levers wildly. "Right. Paris. Does the early nineteenth century sound good? I've been dying to pay Napoleon a visit." He turned off the monitor that he had been studying, pulling it up out of Amy and Rory's view.

"Wait, you mean like _the_ Napoleon?" Rory asked.

"Yes, Rory, h ow many Napoleons are you famil iar with?" The Doctor said, now pushing buttons.

As Rory started to utter a comeback, Amy interjected, "Oooh, Doctor, we can go see the Eiffel Tower, yeah?"

Rory rolled his eyes. "Amy, honestly, did you ever pay even the slightest bit of attention in history class? Napoleon was dead years before they built The Eiffel Tower."

"Right you are, Mr. Pond! But don't worry you lot, we can do much better than some musty old tower," The Doctor grinned excitedly.

Suddenly, the TARDIS began to shake so violently it seemed as if it had crashed into a boulder. Amy let out a scream and both she and Rory instinctively grabbed for the platform railing. The Doctor held tightly onto the console.

As quickly as the shaking started, it stopped abruptly.

"Um, Doctor, _what _was that?" yelled Rory, running over to Amy to help her up.

"Is everyone OK?" The Doctor walked over to them. "Amy, Rory?"

Amy took Rory's hand and stood up. "Yeah, fine, except for the bruises all over my body," she said in a snarky tone. "Right, then. Let's go meet Napoleon."

"I think we're going to have to take a rain check on that," the Doctor stated, pulling down monitors and running about. "Before we go anywhere, I want to see if there's anything wrong with the TARDIS. She doesn't crash for any old reason."

Amy grunted and sat down on the jump seat. "Just don't take too long."

"Be patient, Pond," The Doctor said offhandedly. "Now, if you two will excuse me, I have to check the TARDIS's interior command circuits. Be back in a tick!" The Doctor dashed into a door right off of the console room that Amy had never seen him go into before.

After a groan and a moment of sitting in bored silence, Amy stood up and walked over to Rory.

"So…" She said, grabbing Rory's hands.

"So…?" Rory responded.

She pulled his hands closer to hers and looked back at the door that The Doctor had left through, guaranteeing that it was closed. "How long d'you think we got until he comes back?"

"Who knows, he could be on Mars by now," Rory replied dryly.

"That's what I wanted to hear," Amy flirted. She wrapped her arms around his neck and kissed him passionately.

Rory returned the gesture, but when they broke away he stared at her dumbfounded. "Um, OK," he began slowly. "Not that I mind, but out of curiosity, what are you –?

Amy threw her head back and laughed. "Rory, you have always been so hopeless," she ruffled her hands through her long ginger hair. "Alright, you, shirt off."

She began unbuttoning her checkered blouse as Rory blushed and pulled away from her frantically, glancing towards the door. "Amy! No way, not _now_!"

"Aw, you're no fun," she fake-pouted, and fell down onto the seat once again. "Well, what are we gonna do till he gets back? Got any bright ideas?"

"Why don't we throw some darts?" Rory suggested. "You know, I still think you're the only person who's ever found a way to _cheat_ in a game of darts."

"You're just mad because I beat you." Amy grinned as she strode over to a square TARDIS compartment where the darts were stored.

Rory took two of the sodas from the package that the Doctor had picked up on his last trip to the planet Messaline. He reached into the ice box under the console where they were stored and raised his eyebrows. "How do you know I didn't let you win?"

"Because I've seen you play at the pub and you were just as rubbish then as you are now."

They ended up playing for the next twenty minutes until the blackboard which they used to keep score read: "Amy - 31 | Rory - 27".

"Not bad," Amy admitted.

"I want a rematch, I think I have a sprained wrist." Rory brooded, cracking a smile when Amy caught his eye.

"Fine, you big baby. But don't come crying to me when I cream you."

Amy started to erase the blackboard when she remembered – wasn't the Doctor supposed to be "checking on the TARDIS"?

"Hey, where do you think the Doctor's got to? He's been gone a long time now." Amy asked, becoming a bit anxious.

"God knows," Rory replied, rolling his eyes once again. "I wouldn't be surprised if he got lost, it's huge in here!" He took a swig of his soda, which he assumed was the Messaline equivalent of grape flavored. "I mean, just the other night, I was out looking for the kitchen when I took a wrong turn – that was the night when we went to Marilyn Monroe's party, so I was still a bit, er, out of it – and I found myself in a bloody ice rink with a –"

"Rory," Amy interjected.

He stopped short. "Yeah?"

"Shut up," She replied, her lips curving into a smile. "I'm worried."

Just then, the same door that Amy saw the Doctor leave through opened. Out walked the Doctor, stiff and looking slightly paler than usual. His bowtie was crooked and there was something strange about the way he walked.

"Oi! Where have you been?" Amy teased. "You missed it, I gave Rory another lesson on how to play darts without being a moron."

The Doctor didn't grin back, but simply walked unenthusiastically to the console and pulled some levers.

"Jeez, somebody is being a Mr. Grumpy-pants today," Amy looked the Doctor over, growing slightly concerned. "You alright?"

"Yes, Amelia, I'm fine!" The Doctor replied in an oddly cold manner, turning his back from her.

Rory and Amy exchanged a look, and Amy started again: "Oooh-kayy…so, what was wrong with the TARDIS? Did you find anything?"

The Doctor turned his head towards Amy. "The TARDIS?" He looked muddled.

"Yeah, you wanted to go and check some command-y thing…" Rory reminded him, but stopped when Amy shot him a be-quiet-you're-not-helping look.

She took a step towards the Doctor, speaking tenderly. "Look, if there's something wrong, you can tell me. I mean, you can trust us…"

The Doctor glared at her and began fiddling with various instruments on the console.

Determined to get some sort of answer, Amy persisted, "What was in that room you just came from? I don't remember seeing you ever go –"

"Is it so difficult for you to shut that fat mouth of yours once in a while? It's giving me a headache!" yelled the Doctor abruptly in an unusually apathetic tone.

Amy, confused at his behavior but still stubborn as ever, quickly replied, "Sorry, I was just worried –"

"Have you gained weight?" The Doctor interrupted her yet again. "You look different, and not a good different."

Taken aback, Amy laughed awkwardly. "What? Uh, no...no I don't think so, why –?"

Rory fixed his eyes on the Doctor as if sending a silent "knock it off". Amy was completely baffled.

"You know, you don't _scare_ me, Rory," The Doctor smirked, getting his message. "You sure think you're something, don't you?"

"Huh?" Rory asked, getting a bit irritated with the Doctor's rudeness.

The Doctor continued casually, leaning up against the console. His anger from a few moments ago seemed to have evolved into insolence. "You know, maybe it's your hair Amy, have you done something different to it? It doesn't do you justice."

"What's wrong with my hair?" Amy asked, feeling both insulted and embarrassed.

"Amy, _nothing_. Ignore him," Rory growled.

The Doctor turned away from them, as if he were growing bored. "Oh, Rory, Rory, Rory. You are even a bigger fool than I thought. You know, when I first met you, I didn't like you at all, and now –"

"OK, Doctor, stop!" Amy shouted suddenly. "What is this? What's the matter with you?" She placed a hand gently on his shoulder, and said softly, "It's like you're not even yourself –"

"SHUT UP, JUST SHUT UP!" The Doctor screamed, suddenly furious again. He turned himself around to look Amy in the eyes and slapped her violently across the face. "WILL YOU JUST LEAVE ME ALONE, YOU IDIOT!"


	2. Chapter 2

The Doctor then roughly shoved Amy towards the ground and started to stalk off.

"Oh my god!" Rory caught her just in time, resisting the urge to strangle the Doctor. Before Rory had the chance to act, Amy pushed Rory's hands away and stared at the Doctor, holding her hand to her stinging face.

"I…" Amy just stood there, at a loss for words, and tried to fathom what he had just done. She kept looking up at him, her best friend, and tears flooded her eyes. The Doctor had never talked to her like that before. The Doctor had never _hurt_ her before. Why did he suddenly get so angry? What had _she _done? The goofy man who made her laugh, his sweet smile that never failed to cheer her up when she was down. Those big, sad, caring eyes. The person standing before her was not that man.

"St-stay away from me!" she stuttered, tears flooding her face. She turned and ran out of the console room, hiding her face, and sprinted down the hallway where her and Rory's bedroom was located.

Rory was shaking with anger. _No one lays a hand on Amy. _He ran at The Doctor and punched him across the face. "YOU NEVER COME NEAR MY WIFE AGAIN!"

The Doctor, lip bleeding and still raging as well, grabbed Rory's shirt front and punched him back hard in the nose , knocking him to the floor.

Rory hit the floor with a thud, his limbs aching. He could feel the warm blood running out of his fractured nose. He got back on his feet as fast as he could.

"What the _hell_ is wrong with you?!" Rory shouted at the Doctor, who was standing there blankly once again. _What is going on?_

"Amy...Amy!" he said to himself as if he was just remembering that she had ran out of the room. Rory, holding his nose, dashed into the corridor where their room could be found.

When he reached their room, he threw open the door and scanned the large space for Amy. He found her sitting on the edge of their newly-obtained double bed, weeping gently into her hands. Rory hated seeing Amy cry. He gently closed the door behind him and flipped the lock.

Amy jumped up when she noticed him, startled. Her eyes scanned over Rory's bruised and bloodied face.

"Oh, Rory," she cried, running into his arms.

Rory clutched her shaking body against him as she sobbed. "I'm so sorry, Amy," he said gently, stroking her long orange hair soothingly.

Amy lifted her head back up and cupped Rory's face with her hand. "What did you do? Please tell me you didn't get into a fight, you big idiot," she smiled through her tears.

"Don't worry about me," he replied, returning Amy's weak grin. "Are you alright?"

Her left cheek appeared to be bruised and swollen. She frowned. "Yeah...yeah, I'm fine," she said, wiping the tears off her face. "Just shaken, that's all. I don't know why he –"

Rory pulled away and looked into her eyes. "Amy, I promise, he won't hurt you again. I'll make sure of it."

She looked down at her feet with watery eyes, attempting to wipe her tears away to no avail.

He began again slowly, "We need to get you some ice to keep down the swelling."

Amy reached her hand up and felt Rory's nose. "No, let me take care of you first, you're an absolute mess. Your nose is even more out of place than usual," she teased and Rory laughed.

"Right. OK. Maybe that's not such a bad idea after all." he agreed, looking into the mirror over their wardrobe.

Amy wetted a cloth from their washroom and sat Rory down on the end of their bed. She joined him and dabbed at the blood coming from his nose until the flow yielded.

"Rory?" Amy said after a few moments of silence.

Rory, cringing from the pressure on his sore face, managed to respond, "Hmm?"

She paused for a moment. "It doesn't make any sense."

He took the now-red cloth from her and brought it over to their sink. "I know," he said blankly, his back to her. Rory turned on the water and began washing off the cloth.

Amy started over. "It's just – I don't – I don't get why he got so mad, and...he's just never hurt me."

Rory heard her voice crack on the last two words. He left the cloth in the sink and sat down beside her, clutching her hands in his. "Amy, we don't have to talk about this right now. What's important is that we're both safe." He took a deep breath and then continued, "I think...I'm going to start packing our things. You don't have to help if you aren't feeling well, but – Amy, we need to leave."

_Leave?_ Amy thought, shocked. She couldn't imagine leaving the Doctor now, after everything they've been through, after all the times he's saved their lives, after he had become Amy's best friend. Especially after just one outburst. He could've just been really mad at something, right?

"No, no, we're not leaving him," Amy pulled her hands out of Rory's and stood up. "We can't, Rory, we just can't."

"Amy…" Rory followed after her. "Amy, you saw –"

"What if there's something wrong with him, Rory?" she yelled with passion and fear. "I mean, that was just five minutes ago! We can't leave him so fast, you're being rash!"

Becoming frustrated, Rory yelled back, "Amy, he slapped you across the face! Be sensible, we need to get out of here!"

"Don't tell me what to do, Rory!" Amy replied, growing increasingly frustrated by the minute. _Can't Rory see that the Doctor isn't himself? What if he's sick, and that's why he's acting this way?_

Rory grabbed her wrist. "Amy, look at me –"

"Get away from me!" she shouted, tugging her hand back and storming away from him.

Rory ran his hands down his face, exhaling. "What else are we supposed to do, then?" he threw himself down onto their loveseat. "Do you have any bright ideas? Because we can't stay in here forever, and we can't keep traveling with the Doctor if he's going to keep acting like a lunatic!"

Amy folded her arms. "He's not a lunatic," she said in a small voice.

Rory let out a sigh of exasperation.

"Let me finish!" Amy demanded. "I mean, he was acting all normal till he went into that room, yeah?"

"If you can ever consider him normal, then sure." Rory replied in a snarky tone.

"Shut up, you know what I mean," Amy took a seat next to him, thinking. "It's just...I thought that maybe something happened in that room, you know. Maybe he has an evil clone, or...or got bit by a space bug or something."

Rory's nose began to bleed again. He tilted his head back and held onto his nose. "I was actually thinking about that too," he conceded. "But even if that's the case, how are we supposed to 'make him all better' without him going all mental on us again?"

"I know, I know, but we can't just leave him alone if he's out of his right mind," Amy replied, shaking her head.

They sat for a moment in silence, both thinking hard, until Rory spoke. "What if...maybe…no, never mind."

"What?" Amy rounded on him. "What is it? Did you have an idea? Tell me!"

Rory stood up quickly. "Uh, no...no, it was stupid, forget it, OK?"

"Well, now I _have_ to know," Amy replied, getting up on her feet as well.

He began pacing back and forth. "Well, it's just that – Amy, what do you think is in that room that the Doctor went into before he went all mad?"

"I don't know, anything, I guess," she replied.

"Right…I just thought that if we were to see what was in there, see if there was something that made him act this way...then maybe we could figure out the problem," Rory finished.

A wide, hopeful smile appeared on Amy's face. "Of course! That's brilliant!" she ran towards him and kissed him on the cheek. "Come on, let's go before it's too late…" she took her chocolate brown leather jacket out of their wardrobe and started putting her arms through the holes.

Rory wasn't as thrilled. "Wait, slow down Amy. Shouldn't we, you know, make a plan first?"

Amy began re-tying her shoelaces. "Right, here's the plan: we get to the console room, we go through the spooky door, and we find out what's inside, yeah?"

"Fine," Rory sighed, unlocking the door. "But we have to, you know…be careful around him,"

"I know," Amy said in a more serious tone, seeing the look of concern on his face. "We'll be careful."


	3. Chapter 3

Amy, pulling Rory by the hand behind her, walked slowly and quietly through the TARDIS corridor that lead to the control room. It was not a long walk if you knew the right way; thankfully, they'd both gone this route so many times that they knew all of the twists and turns like the back of their hands.

Soon, Amy recognized the golden light coming through the archway at the end of the passage that went through to the console room. Tiptoeing, her and Rory sneaked up to either side of the archway and peered through.

"Do you see him?" Rory whispered.

Amy replied a bit louder, "No, it doesn't seem like he's anywhere in –"

"SHH!" Rory pressed a finger to his lips and it was Amy's turn to roll her eyes. He continued, "Right, OK, I didn't see him either. Now let's go see what's in that room."

Walking quietly through the archway and into the console room, Rory and Amy inched over to the door that the Doctor has gone through only an hour earlier.

Rory pulled on the door handle. "Dammit, it's locked!" he muttered.

"Not for long," Amy winked at him and slipped a bobby pin out of her hair. She bent and stuck it into the lock, twisting and turning the tip.

"Like that's going to work, this is a time machine!" Rory droned.

As Amy had predicted, the lock had turned with a _click_ and the door handle opened right up.

She turned her head around at Rory. "Don't underestimate me, Mr. Pond."

Rory let slip a small grin as Amy opened the door further. They carefully walked into the pitch-black room and closed the door behind them.

"It's bloody dark," Rory pointed out the obvious. "Can you see anything?"

"No, can you?" Amy replied, feeling around with her hands, trying to locate Rory. She found his hand and held onto it. "Do you have a torch with you?"

"No, I didn't know we would be exploring pitch-black creepy Alien rooms today, did _you_?" Rory replied.

"Quiet, help me find the lights." With her free hand, Amy felt up and down the cold walls, hoping to find some sort of on-off switch. Rory did the same.

"Found one," Rory announced, flipping on what he felt was some oversized, oddly-shaped kind of light switch. The room lit up.

It was huge. The walls were covered with the similar golden hexagonal-shapes that were in the main console room. There were all sorts of futuristic gadgets, some on the walls and some rooted to the floor. It seemed like it was a kind of second, more complicated control room.

"Now I can understand how the Doctor managed to spend half an hour in here," Rory said, looking around. "This is gigantic! Here I was, thinking it was a broom cupboard..."

"Rory…" Amy tugged on his arm.

He turned around. "What?"

Rory then realized what Amy was looking at: there, in a corner of the room, was the Doctor, sprawled out on his back, seemingly unconscious.

Amy bolted over to him and knelt down, feeling his chest.

"Rory!" she screamed. "Rory, come here! I – I can't feel a pulse."

Rory dashed over to where The Doctor lay, got down on one knee beside Amy, and felt his wrist.

"Rory," Amy began tearfully. "Tell me he's alive."

"I can feel a pulse, but it's no wonder you didn't because it's not very strong," Rory replied, furrowing his brow. He then attempted to listen for a heartbeat.

"What does that mean?!" Amy yelled as she held the Doctors head in her hands. "Help him!"

"Amy, calm down, I'm trying," Rory could hear two small but weak heartbeats on The Doctor's chest. "His hearts are beating, but just barely."

Amy looked up. "What's wrong with him?"

Rory scratched his face, thinking. "I-I don't know. I don't know what's normal for his body and what isn't!" He felt The Doctor's cold face. "He's definitely breathing."

"Should we check him for injuries? Could he have a concussion?" Amy asked.

Rory drew his attention to The Doctor's head. "If he does, I'm not seeing any form of bruising or injury. I don't think that the issue's anything internal, like a heart-attack, because he isn't showing any symptoms."

Amy bit her fingernails. "Well, can't you fix him anyway?" she ordered frantically.

"I can't if I don't know what's wrong, Amy, it doesn't make any sense!" he said, starting to get worried himself.

Amy wrapped her arms around the Doctor's neck and lay her head on his chest, fresh tears leaking down her cheeks. Rory gave Amy a comforting squeeze on the shoulder before he continued to examine the Doctor in any way he could think of.

"Please, please wake up," she cried.

All of a sudden, the Doctor's eyes popped open. Amy screamed and both she and Rory jumped in alarm.

"Doctor…?" Amy began cautiously, afraid that he would snap at her like he did before.

The Doctor sat up precipitously. "Hello, Amy. Wait – Amy! Rory!" He looked around and saw Rory there as well. "Are you alright? How long have I been out for?"

Amy and Rory instinctively stood up, unsure whether they could trust him, and they exchanged a look.

The Doctor caught Amy's eye and looked her up and down. "What's happened to your face?" He jumped to his feet and looked at her more closely. "Did someone hurt you?"

Rory, feeling once again the rage that was inside of him merely half an hour ago, took a step in front of Amy. "Is this some kind of joke to you?"

The Doctor looked from Rory to Amy, confused. Rory's face was beaten up worse than Amy's. "I'm not joking, what happened to you two?"

Rory, fuming, quickly advanced towards the Doctor.

"Rory, stop!" Amy caught hold of him before he could charge.

The Doctor put his hands up and took a few steps back, unsure of what he had done to provoke Rory. "Why are two so upset with me? What did I do?" he asked honestly.

"What did you do?" Rory said in a quiet but trembling voice. "You insult my wife and then you _physically hurt_ her, Doctor, and you're asking me _what you did_."

"What?" The Doctor blinked, his attention on Amy's swollen cheek once again. "You think _I_ did that?" He walked towards Amy. "Rory, I would _never_ –"

"Don't you dare go near her," Rory hissed.

"Rory, don't," Amy said, pulling him back and whispering in his ear. "I don't think he can remember anything."

"I don't care if he can't remember it! It still happened!" Rory whispered back loudly.

The Doctor still looked bewildered. "What can't I remember?" he asked, curious for a response.

Amy broke her whisper, too excited to contain her secretiveness. "See, Rory? Look, he's clueless!" she laughed as relief washed over her like a wave. "He must've been possessed or something, I told you!"

"What? Wait, _what_?" The Doctor's face contorted as if he had just remembered something. "No, oh, I'm so stupid!" He hit himself across the face. "Stupid, stupid, _stupid_!"

He began pacing around the room, scratching his jaw. Suddenly, he made a turn and rounded on Amy again.

"Amy, tell me the truth, did _I _cause that bruise on your face?" he asked her seriously.

Amy slowly nodded. Once again, she couldn't tell what was going on with him.

The Doctor turned to Rory. "Rory, is your nose all funny because of me? Did we get into a fight?"

Rory nodded as well, just as baffled as Amy and unsure of what to say.

The Doctor held his face in his hands and shook his head. "Oh, no, no, NO! This wasn't supposed to happen!" He looked back up at Amy and Rory. "Rory – Amy – I'm sorry. This was all my fault."

"What?" Amy asked, her heart sinking.

The Doctor began, speaking quickly, "I came in here after the TARDIS shook and I stumbled upon this – er – experiment that I was working on earlier by mistake. As I was checking on the TARDIS's inner-extractor volume, I accidentally stuck my hand in a pot of the Fle – the, the um, the experimental substance, and it took a sample of my DNA.

"This – substance – can make a living, uh, clone, in a way, when it has your DNA. It usually works, or I think it works, fairly well, but I hadn't checked the radiation levels of it in a couple of days and, well, I suppose it went bad."

"Sorry, no, not following," Rory said, shaking his head.

"Let me finish," The Doctor began pacing once again, and explained, "This substance created a copy of me, in a way. I had been studying ways to undo the process, but before I had a chance to stop him, he must have knocked me unconscious."

Amy put her hand on her hip. "Hold on, within thirty minutes you managed to _clone_ yourself. That's pretty impressive, even by your standards." She could feel her mood increasing by the second. _Her_ Doctor was back.

The Doctor began digging through piles of odd mechanisms. "Yes, well, I'm still not sure how he managed to knock me out." He pulled out what looked like an electrical syringe. It was large and had a small amount of bluish liquid inside towards the bottom. "Here we are. Your standard Calisto B stun injection. You inject liquefied Telos minerals into the victim, rendering them unconscious for a period of time, depending on how much you inject, of course."

Rory began slowly, trying to understand. "So...so he stabbed you with that thing."

"No, Rory, I just told you. It's an _injection_, not a knife," The Doctor tapped Rory lightly on the head with the syringe. "And given that this was full the last time I saw it…" He examined the small drops of liquid at the bottom of the syringe, "...I'd say he gave me enough of this juice to make me sleep for, oh, one hour, maybe longer?"

"That's about how long you've been gone." Amy nodded, a smile growing across her face. She had been right. _He would never hurt me_. _I knew it wasn't him_.

She couldn't hold back any longer. Amy impulsively ran towards the Doctor and flung her arms around his neck. "I'm so happy to see you!" she laughed, hugging him tightly. "Don't ever do this to us again!"

"I won't," The Doctor patted her back fondly. "But we need to focus, Amy, Rory, because the clone is still somewhere in the TARDIS. If what you told me is true, then I think that its motive was to act insane and make you two want to leave so that he could have the TARDIS to himself."

"We wouldn't do that, Doctor," Amy broke away.

"Oh, Amelia," The Doctor beamed at her. "You trust me a whole lot more than is good for you."

Rory felt a pang of guilt. He still managed to ask, "He, uh, also sort of had these mood swings. Like, one second he would be angry, then blank, then a complete git."

The Doctor shrugged, still smiling at Amy. "If he really wanted you two to leave him, then sure, I wouldn't put it past him. That sounds like a tactic to me."

"Well, talking about him won't help us get rid of him," Amy chimed in. "So, how do we find him, Doctor?"

The Doctor looked like he was debating something in his head. "Er – not _we_, Amy, _I_," The Doctor spoke slowly. "This was my fault, and now I have to fix it. Given his dangerous nature, I, um, I think it best that you two stay put."

"Right, because we've never done anything dangerous before," Rory replied.

Amy joined in his protest. "Yeah, if you're going anywhere, Rory and I are coming too."

Desperately, the Doctor persisted, "No, no you're not, you can't – erm – why don't you two go and play f ootsie back in the console room, and I'll be back before you know it," he started towards th e door.

"Doctor!" Amy shouted after him. "What aren't you telling us?"

He hesitated for a moment, gazing directly at Amy. "Nothing, Amy. I promise. It's just that…well, the clone reversal process is a bit...not very nice. I don't expect I'll need any help so I don't see the point in bringing you too along," he lied.

Amy, frowning, still looked skeptical.

"Really, I'll be back in just a mo'. Wait in the control room. You won't even know I'm gone." He smiled and strode out the door.

"Uhhhhrr!" Amy groaned once the Doctor had left. "I can't help but feel like there's always something he's not telling us, especially lately."

Rory nodded in agreement. He was still processing everything that the Doctor had just told them.

"It's just so frustrating. I can never tell when he's lying and when he's actually telling the truth."

"I know the feeling," Rory muttered.


	4. Chapter 4

The Doctor walked the halls of the TARDIS, using a handheld body heat scanner to detect the fake Doctor. He had been searching for only five minutes, but he was already frustrated with the difficulty of this task.

"If I were a Flesh replica of myself, where would I go to hide?" he said to himself.

He did not want this process to last much longer, for Amy and Rory would become even more suspicious of him. They couldn't know what the "clone" really was – a Ganger, a Flesh replica, what Amy has been for the past eight months. Not now, anyway; it was too soon.

"Hello, Me," The Doctor was met face-to-face with his accidental Ganger. The Ganger's face was whiter than his own, and his posture looked awfully different as well. He also had the beginnings of a black eye, and the rest of his face looked beaten-up.

The Ganger sputtered, "Aren't you supposed to be unconscious?"

"OK, so evil Flesh replicas aren't the best at greetings, I'll take note," the Doctor replied nonchalantly, digging in his pockets for his Sonic.

"If you're going to try and stop me, it's useless!" The Ganger shouted. His personality was strangely unlike the Doctor's. "Your companions already think you're a lunatic, and frankly, they're right. You have a lot of nasty secrets in your head, don't you?"

"I'm sorry," The Doctor said in a completely different tone, his screwdriver in his right hand, behind his back.

The Ganger stared at him. "What?" he uttered.

In a flash on events, the Doctor pointed his screwdriver at his Ganger and held down two manual functions. The tip glowed green and the Ganger dissolved into a thick, milky white liquid, a puddle on the floor.

The Doctor kept himself from staring at the puddle for long. He felt tired and wary as he strode away from the spot, not looking back. He soon reached the console room, his head clouded.

"Amy! I'm back!" He called, putting on a different mood. The room was empty. "One request, just one. 'Stay in the console room,' I said. 'OK sure, Doctor,' they said. _Every time_. Honestly…" The Doctor grumbled.

He decided that they would most likely be waiting in the room which he had left them. He opened the door and stepped inside. "Amy? Rory?" he called.

They were standing off to the side of the room, kissing each other furiously, their hands running in places that the Doctor had no desire to witness. He rolled his eyes, also noticing Rory's hair disheveled from Amy's hands and her leg around his waist. They jumped and broke apart immediately when they heard the Doctor's voice.

"Hi," Amy greeted, blushing madly.

Rory glared over at her as if she was at fault for something, to which she replied with an apologetic grin.

"Seriously? I leave for ten minutes and you decide it's a good time for a snog," The Doctor said, half-annoyed and half-embarrassed himself.

Rory awkwardly started sorting out his messy hair, needing something to do to defuse the tension. Amy mock-scowled at The Doctor.

"So, did you find him then? The 'evil clone' version of you?" Amy asked, genuinely interested.

Rory was still trying to pretend that he wasn't there.

The Doctor shifted his hands. "Yes," he replied softly. "And you were right, he did have a bit of fight in him…"

"Wait, so you fought him?" Rory finally piped up, the redness in his cheeks disappearing.

"Well, it wasn't much of a fight. Nice punch by the way, Rory, he had a black eye," The Doctor grinned at Rory. "We don't have to worry about him anymore because I...disassembled him right away." He cringed, hoping (but not expecting) that they would stop asking questions.

As the Doctor had predicted, Amy retorted, "How do you just "disassemble" somebody? He wasn't, like, a robot, yeah?"

The Doctor's smile grew wider as he turned his attention back to Amy. "No, Pond, use your head. Of course he wasn't a robot, he was...a type of matter. A chemical experiment gone wrong. But nothing to be worried over now," he quickly added.

"Ookayy...I wasn't, but thanks." She returned his smile and the Doctor felt a wave of guilt wash over him. It increased as he once again noticed the bruises on her and Rory's faces.

Rory stepped forward, his hands in his pockets. "So, Paris, then?"

"Right, Paris!" The Doctor clapped his hands together. "But first, are you sure you don't want to take a break in the Med Bay for a while? The TARDIS can help take care of those bruises, I just picked up this oil from Shallacatop that's supposed to have wondrous healing powers..."

"No, I'm fine, just a bit sore, that's all," Amy responded happily. "How about you, Rory?"

Rory felt his nose. "Yeah, I think I'm alright for now. I'll just, you know, try not to get into another fist fight anytime soon."

Amy laughed but The Doctor frowned. "I'm sorry, Rory, Amy. It was really my fault that you're hurt."

"No, it wasn't," Amy walked forward and kissed him on the cheek. "Well, maybe it was, but we're not blaming you for it."

"Well, good," The Doctor replied. "Come on, if you both are feeling up to it, I think a picnic at the _Jardin des Plantes _would be nice, what do you say?"

"It think it sounds great," Amy said.

"Brilliant." The Doctor led the way back into the console room, Amy and Rory following behind.


	5. Chapter 5, Epilogue

The Doctor took a sip of his chardonnay, and as usual, spit it back into his glass with a sour look on his face.

"I don't know how you can stand this stuff," he groaned, inspecting the wine bottle.

"It's kind of an acquired taste," Rory replied, drinking some from his own glass. "You get used to it."

They were sitting atop a classic gingham picnic blanket at the Jardin des Plantes in Paris. The park officials apparently owed the Doctor a few favors and allowed him and his friends to dine anywhere within the botanical garden. It was the year 1810, the Doctor adamant on paying Napoleon a visit once they had finished eating. He and Rory were left alone on the blanket as Amy insisted on taking some pictures around the park, telling Rory that some photographs of flowers "would look great above the mantel".

"There's still one thing I don't understand," Rory began. "Why did the TARDIS start crashing when you didn't find any problems with it? Or did you?"

"That was just her way of telling me that something was not right," the Doctor answered. "In this case, it was the fact that a baddie clone of mine was loose,"

"But the TARDIS shook before the clone was even created," Rory countered.

He gave a half-smile. "The TARDIS is a time-machine, Rory."

Then the Doctor, giving up on his wine, put the bottle aside and lay down on the blanket, gazing up at the clouds and squinting at the sun in his eyes.

Rory finished his glass and the two sat in silence for a few minutes until Rory finally said, "Doctor?"

"Yes, Rory?" The Doctor replied lackadaisically, still lying on his back.

Rory had something on his mind that he was itching to get out. "Remember what you said earlier, to Amy, about how the clone tried to get us to leave the TARDIS?"

The Doctor sat up. "Yes, I think so. Why?"

"Well…" Rory started, fumbling with his wedding ring. "After the clone version of you attacked Amy – and me too – I...told her we should go home."

"Oh," The Doctor replied blankly.

Rory was now the one who felt guilty. "She said no, of course, she wasn't leaving you. She insisted that you would never act that way, and that something must've been wrong with you."

The Doctor smiled. "Good ol' Amy."

"Yeah," Rory continued, "And I think I believed her, but I just didn't know what to do. I was going to make you – or, your clone, I guess – take us back to Leadworth if we didn't come up with a plan. Thankfully, we did and we found you unconscious," Rory looked the Doctor in the eyes. "I'm sorry I doubted you, Doctor. I don't know how I could think you would do those things, after all you've done for us, and you've saved our lives so many times –"

"Rory, it's fine." The Doctor insisted. "The clone was dangerous, he hurt Amy...to tell you the truth, I'd be concerned if you weren't skeptical."

Rory looked down again and continued to fumble. "I don't think it's fine. I was being stupid. I mean, if we had gone home...what would have happened to you?"

"I would've woken up, found the clone, and taken the TARDIS back to Leadworth to apologize to you and Amy," the Doctor reassured him. "Rory, you did nothing wrong. You were worried, rightfully so. I don't blame you."

"Thanks," Rory replied. "I just...I'm still sorry. Amy trusts you, you know?"

The Doctor suddenly felt a pang in the pit of his stomach. "I know."

"And-and I do too. I should've known you wouldn't do anything to hurt her, or us for that matter."

His words were killing the Doctor on the inside because he knew that he was going to have to wake up the real Amy soon, and tell both of them the truth. All he could manage to say to Rory in response was a genuine "thanks".

Amy strolled back over to the Doctor and Rory with a camera full of pictures that were sure to look good framed above her and Rory's mantelpiece. As she got closer, she grinned when she saw that they were talking. She came up behind them, hearing the Doctor muttering a "thanks" for who-knows-what.

"Hey," Amy said happily to announce her presence and sat down between the Doctor and Rory.

"Joining us again, Pond?" The Doctor said in a cheery tone, though he looked oddly flushed.

"So I am. What did you two get up to while I was gone? I heard you talking," she said as she turned on her camera in her lap and scrolled through the photos.

"Oh, you know, manly things," Rory teased. "Did you get your pictures?"

He leaned over to get a closer look at her camera screen, put she pushed his face away playfully.

"Yep," she replied in a proud manner. "But I'll show you them when we get back to the TARDIS. Right now I want to meet Mr. Bonaparte."

The three of them packed up their picnic supplies into a wicker basket which Amy carried. They began walking towards the exit of the garden when Amy suddenly dropped the basket, resulting in a loud _clash_ from the dishes inside.

"Oww, ow!" she moaned. A terribly sharp, burning pain had erupted in her lower back. She flinched and placed her hand there, trying to soothe the discomfort.

"Whoa, what's wrong?" Rory asked worriedly, placing a hand underneath her arm to help her balance. The Doctor did the same on her other side, knowing exactly what was wrong.

"Uh – sorry, nothing, nothing, I'm fine," she cringed. "My lower back just hurts, I probably pulled a muscle earlier today."

"Well, you don't seem fine, if it hurt so bad that it made you drop the basket," Rory put his hand on top of hers in the small of her back, rubbing it softly. "Amy, if think you pulled a muscle, maybe we should go back to the TARDIS and you could lay down for a while. I might have some pain relievers back in our room…"

Amy waved him away. "No, I'm alright, now it just feels a bit sore, maybe it was just a cramp or something, let's keep going."

"Are you sure?" The Doctor asked, concerned as well, picking up the basket off of the ground.

"Yeah, we can come back here any time we want," Rory said kindly, still with a hand on her back.

Amy shook her head and stood up straight. "No, let's keep going. I'm feeling better, I swear." She smiled at The Doctor, who forced a smile back.

They continued walking with no problems, Amy and Rory chatting amongst themselves. _No, no, it's happening sooner than I expected_, the Doctor thought. _I need to find more information on The Flesh as soon as I can_.

They enjoyed the rest of their time in Paris, not coming across any dangers. However, the Doctor knew that there was one coming that he couldn't prevent.

4


End file.
